#install_github(“jokergoo/ComplexHeatmap”) Didn’t install #didn’t install BiocManager::install(“inveRsion”)

Load packages and data

library(devtools)
## Loading required package: usethis
library(bigstatsr)
library(bigsnpr)
library(ggplot2)
library(OutFLANK)
## Loading required package: qvalue
library(vegan)
## Loading required package: permute
## 
## Attaching package: 'permute'
## The following object is masked from 'package:devtools':
## 
##     check
## Loading required package: lattice
## This is vegan 2.6-6.1
library(pheatmap)
sessionInfo()
## R version 4.4.0 (2024-04-24)
## Platform: x86_64-apple-darwin20
## Running under: macOS Sonoma 14.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] pheatmap_1.0.12  vegan_2.6-6.1    lattice_0.22-6   permute_0.9-7   
##  [5] OutFLANK_0.2     qvalue_2.36.0    ggplot2_3.5.1    bigsnpr_1.12.2  
##  [9] bigstatsr_1.5.12 devtools_2.4.5   usethis_2.2.3   
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.5       xfun_0.44          bslib_0.7.0        htmlwidgets_1.6.4 
##  [5] remotes_2.5.0      bigassertr_0.1.6   vctrs_0.6.5        tools_4.4.0       
##  [9] generics_0.1.3     parallel_4.4.0     tibble_3.2.1       fansi_1.0.6       
## [13] cluster_2.1.6      pkgconfig_2.0.3    Matrix_1.7-0       data.table_1.15.4 
## [17] RColorBrewer_1.1-3 rngtools_1.5.2     lifecycle_1.0.4    compiler_4.4.0    
## [21] stringr_1.5.1      munsell_0.5.1      bigparallelr_0.3.2 codetools_0.2-20  
## [25] httpuv_1.6.15      htmltools_0.5.8.1  sass_0.4.9         yaml_2.3.8        
## [29] later_1.3.2        pillar_1.9.0       jquerylib_0.1.4    urlchecker_1.0.1  
## [33] MASS_7.3-60.2      ellipsis_0.3.2     cachem_1.1.0       doRNG_1.8.6       
## [37] sessioninfo_1.2.2  iterators_1.0.14   foreach_1.5.2      nlme_3.1-164      
## [41] mime_0.12          tidyselect_1.2.1   digest_0.6.35      stringi_1.8.4     
## [45] reshape2_1.4.4     dplyr_1.1.4        purrr_1.0.2        splines_4.4.0     
## [49] cowplot_1.1.3      fastmap_1.2.0      grid_4.4.0         colorspace_2.1-0  
## [53] cli_3.6.2          magrittr_2.0.3     pkgbuild_1.4.4     utf8_1.2.4        
## [57] withr_3.0.0        scales_1.3.0       promises_1.3.0     rmarkdown_2.27    
## [61] bigsparser_0.6.1   memoise_2.0.1      shiny_1.8.1.1      evaluate_0.23     
## [65] knitr_1.46         doParallel_1.0.17  miniUI_0.1.1.1     mgcv_1.9-1        
## [69] profvis_0.3.8      rlang_1.1.3        Rcpp_1.0.12        xtable_1.8-4      
## [73] glue_1.7.0         pkgload_1.3.4      rstudioapi_0.16.0  jsonlite_1.8.8    
## [77] plyr_1.8.9         R6_2.5.1           fs_1.6.4           flock_0.7
datadir <- "/Users/lotterhos/Library/CloudStorage/GoogleDrive-k.lotterhos@gmail.com/.shortcut-targets-by-id/1DPJy8RgFslz3_PSZLLl7Z21mCvQUvnJZ/Manuscripts/Cod Ecotypes GoM /data/"

bigSNP <- snp_attach(paste0(datadir,  "acod_merged.MAF05_QC.rds"))

#  drop the individual at the 17th position because it is a duplicate. 
#It was a fish that was right in the middle of being red or olive and 
#it accidentally got left in both groups and got sequenced twice. 

G_full <- bigSNP$genotypes[-17,]
pos_full <- bigSNP$map$physical.pos
samp_full <- bigSNP$fam$sample.ID[-17]
pop_full <- bigSNP$fam$family.ID[-17]
chrom_full <- bigSNP$map$chromosome

unique(chrom_full)
##  [1] "NC_044048.1" "NC_044049.1" "NC_044050.1" "NC_044051.1" "NC_044052.1"
##  [6] "NC_044053.1" "NC_044054.1" "NC_044055.1" "NC_044056.1" "NC_044057.1"
## [11] "NC_044058.1" "NC_044059.1" "NC_044060.1" "NC_044061.1" "NC_044062.1"
## [16] "NC_044063.1" "NC_044064.1" "NC_044065.1" "NC_044066.1" "NC_044067.1"
## [21] "NC_044068.1" "NC_044069.1" "NC_044070.1"
dim(G_full)
## [1]     294 2094293
NCORES <- nb_cores()

head(bigSNP$fam)
##   family.ID sample.ID paternal.ID maternal.ID sex affection
## 1      Pop1     16216           0           0   0        -9
## 2      Pop1     16220           0           0   0        -9
## 3      Pop1     16224           0           0   0        -9
## 4      Pop1     16225           0           0   0        -9
## 5      Pop1     16229           0           0   0        -9
## 6      Pop1     16231           0           0   0        -9
head(samp_full)
## [1] 16216 16220 16224 16225 16229 16231
pop.names <- paste0("Pop", 1:9)
pop.IDs<- c("GoM.Mass.Olive.Winter", 
            "GoM.Mass.Red", 
            "GoM.Mass.Olive.Unknown", 
            "GoM.Cashes.Olive", 
            "GoM.Cashes.Red",
            "Ice.Off.SW", 
            "Ice.Near.SW", 
            "Ice.Off.NE", 
            "Ice.Near.NE")
pop.IDs2 <- c("GoM Nearshore Olive - Winter Spawner",
              "GoM Nearshore Red",
              "GoM Nearshore Olive",
              "GoM Nearshore Olive",
              "GoM Nearshore Red",
              "Iceland Offshore",
              "Iceland Nearshore",
              "Iceland Offshore",
              "Iceland Nearshore")
region <- c(rep("GoM", 5), rep("Iceland", 4))
ecotype <- c(rep("Nearshore",5), "Offshore", "Nearshore", 
             "Offshore", "Nearshore")
pop.colors <- c(adjustcolor("darkgreen",1), #mass winter
                adjustcolor("salmon",1), #mass red
                adjustcolor("goldenrod3",0.5), #mass unknown
                adjustcolor("darkgreen",0.75), #cashes olive
                adjustcolor("salmon",0.75), #cashes red
                adjustcolor("darkviolet",1), # Iceland SW Off
                adjustcolor("cornflowerblue",0.5), #Iceland SW Near
                adjustcolor("darkviolet",0.5), #Iceland NE Off
                adjustcolor("cornflowerblue",1) #Iceland NE Near
                )

pop2.colors <- c(adjustcolor("darkgreen",1), #mass winter
                adjustcolor("salmon",1), #mass red
                adjustcolor("darkgreen",0.5), #mass unknown
                adjustcolor("darkgreen",0.5), #cashes olive
                adjustcolor("salmon",1), #cashes red
                adjustcolor("darkviolet",0.75), # Iceland SW Off
                adjustcolor("cornflowerblue",1), #Iceland SW Near
                adjustcolor("darkviolet",0.75), #Iceland NE Off
                adjustcolor("cornflowerblue",1) #Iceland NE Near
                )

write.table(data.frame(pop.names,pop.IDs, pop.colors, region, ecotype, pop.IDs2, pop2.colors), "../outputs/1-Pops.txt", row.names=FALSE)
write("This file contains population-level information
      pop.names: Numbered population ID corresponding to some files
      pop.IDs: Specific Geographic Location
      pop.colors: Color corresponding to pop.IDs
      region: Iceland or GoM
      ecotype: Nearshore or Offshore
      pop.IDs2: An ID based on ecotype and geographic region
      pop2.colors: Color corresponding to pop.IDs2
      ",
      "../outputs/1-Pops.txt.metadata.md")
samp_full <- data.frame(samp_full)

#Remove sample 17, duplicate
samp_full$Pop <- as.factor(bigSNP$fam$family.ID[-17])


# Add population name to smaple dataframe
samp_full$PopID <- factor(samp_full$Pop, ordered=TRUE)
levels(samp_full$PopID) = pop.IDs # this works because the 
# populations are numbered

head(samp_full)
##   samp_full  Pop                 PopID
## 1     16216 Pop1 GoM.Mass.Olive.Winter
## 2     16220 Pop1 GoM.Mass.Olive.Winter
## 3     16224 Pop1 GoM.Mass.Olive.Winter
## 4     16225 Pop1 GoM.Mass.Olive.Winter
## 5     16229 Pop1 GoM.Mass.Olive.Winter
## 6     16231 Pop1 GoM.Mass.Olive.Winter
levels(samp_full$PopID)
## [1] "GoM.Mass.Olive.Winter"  "GoM.Mass.Red"           "GoM.Mass.Olive.Unknown"
## [4] "GoM.Cashes.Olive"       "GoM.Cashes.Red"         "Ice.Off.SW"            
## [7] "Ice.Near.SW"            "Ice.Off.NE"             "Ice.Near.NE"
samp_full$Region <- "GoM"
samp_full$Region[samp_full$Pop %in% c("Pop6", "Pop7",
  "Pop8", "Pop9")] = "Iceland"
samp_full$Ecotype <- "1-Nearshore"
samp_full$Ecotype[samp_full$Pop %in% c("Pop6", "Pop8")] <- "2-Offshore"

samp_full$Region <- as.factor(samp_full$Region)
samp_full$Ecotype <- as.factor(samp_full$Ecotype)
head(samp_full)
##   samp_full  Pop                 PopID Region     Ecotype
## 1     16216 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 2     16220 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 3     16224 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 4     16225 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 5     16229 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 6     16231 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
tail(samp_full)
##     samp_full  Pop       PopID  Region     Ecotype
## 289     18096 Pop9 Ice.Near.NE Iceland 1-Nearshore
## 290     18097 Pop9 Ice.Near.NE Iceland 1-Nearshore
## 291     18098 Pop9 Ice.Near.NE Iceland 1-Nearshore
## 292     18099 Pop9 Ice.Near.NE Iceland 1-Nearshore
## 293     18100 Pop9 Ice.Near.NE Iceland 1-Nearshore
## 294     18101 Pop9 Ice.Near.NE Iceland 1-Nearshore
samp_full$label <- paste(samp_full$Region,samp_full$Ecotype, samp_full$PopID, samp_full$samp_full, sep="_")


### colors for Region and Ecotype ####
samp_full$Region_color <- as.factor(samp_full$Region)
levels(samp_full$Region_color) <- c("blue4", "darkgoldenrod")
samp_full$Region_color <- as.character(samp_full$Region_color) # convert factor back to character 

samp_full$Ecotype_color <- as.factor(samp_full$Ecotype)
levels(samp_full$Ecotype_color) <- c("darkcyan", "seagreen2") 
samp_full$Ecotype_color <- as.character(samp_full$Ecotype_color) # convert factor back to character 

### colors for populations ####
samp_full$PopID_color <- as.factor(samp_full$Pop)
levels(samp_full$PopID_color) <- pop.colors # this works because the populations are ordered by number

samp_full$PopID_color <- as.character(samp_full$PopID_color )
muts <- data.frame(chrom_full, pos_full, Glabel = paste(chrom_full,pos_full, sep="__"))

colnames(G_full) <- muts$Glabel

rownames(G_full) <- samp_full$label

Step 1: Subset data to 50,000 random SNPs and perform PCA.

set.seed(29435798)
index <- sort(sample(1:length(pos_full), 50000))

Gsub <- G_full[,index]


# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012) 

# PCA
# make sure this is run on a code 256 type
# snp object, or it will run forever!
set.seed(6345082)
svd7 <- big_randomSVD(Gsub_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)


# Add PC loadings to sample info
samp_full$Gsub_PC1 <-  svd7$u[,1]
samp_full$Gsub_PC2 <-  svd7$u[,2]

# Add PC loadings to muts
muts$Gsub_PC1 <- muts$Gsub_PC2 <-NA
muts$Gsub_PC1[index] <- svd7$v[,1]
muts$Gsub_PC2[index] <- svd7$v[,2]

#plot(abs(muts$Gsub_PC1), pch=19, col=adjustcolor("blue",0.01))

Perform PCAs on individual linkage groups to identify inversion breakpoints

Chrom 1

index <- sort(which(muts$chrom_full=="NC_044048.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012) 
set.seed(62385534)
svd7 <- big_randomSVD(Gsub_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)

muts$Gsub_LG1_PC1 <- NA
muts$Gsub_LG1_PC1[index] <- svd7$v[,1]

# Chrom 1
plot(muts$pos_full[muts$chrom_full=="NC_044048.1"], 
     abs(muts$Gsub_LG1_PC1[muts$chrom_full=="NC_044048.1"]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG1", ylab="PC1 loading", xlab="position (bp)")

(maxload1 <- quantile(abs(muts$Gsub_LG1_PC1), probs=0.99, na.rm=TRUE))
##         99% 
## 0.006090969
abline(h=maxload1)

#start
LG1start <- min(which(abs(muts$Gsub_LG1_PC1)>maxload1))
LG1end <- max(which(abs(muts$Gsub_LG1_PC1)>maxload1))

muts[LG1start ,]
##        chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 33090 NC_044048.1 11299038 NC_044048.1__11299038       NA       NA  0.006117522
LG1start_minus1MB <- max(which(muts$pos_full<muts$pos_full[LG1start]-1000000 & muts$chrom_full=="NC_044048.1"))
muts[LG1start_minus1MB,]
##        chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 29750 NC_044048.1 10298978 NC_044048.1__10298978       NA       NA 0.0002175627
muts[LG1end,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 104012 NC_044048.1 28292263 NC_044048.1__28292263       NA       NA
##        Gsub_LG1_PC1
## 104012  0.006091121
LG1end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG1end]+1000000 & muts$chrom_full=="NC_044048.1"))
muts[LG1end_plus1MB,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 106154 NC_044048.1 29268531 NC_044048.1__29268531       NA       NA
##         Gsub_LG1_PC1
## 106154 -0.0005602807
plot(muts$pos_full[LG1start_minus1MB:LG1end_plus1MB], 
     abs(muts$Gsub_LG1_PC1[LG1start_minus1MB:LG1end_plus1MB]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG1", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG1start], col="orange", lwd=2)
abline(v=muts$pos_full[LG1end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")

Chrom 2

index <- sort(which(muts$chrom_full=="NC_044049.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012) 
set.seed(235540968)
svd7 <- big_randomSVD(Gsub_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)

muts$Gsub_LG2_PC1 <- NA
muts$Gsub_LG2_PC1[index] <- svd7$v[,1]

# Chrom 2
plot(muts$pos_full[muts$chrom_full=="NC_044049.1"], 
     abs(muts$Gsub_LG2_PC1[muts$chrom_full=="NC_044049.1"]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG2", ylab="PC1 loading", xlab="position (bp)")

(maxload1 <- quantile(abs(muts$Gsub_LG2_PC1), probs=0.99, na.rm=TRUE))
##        99% 
## 0.01020831
abline(h=maxload1)

#start
LG2start <- min(which(abs(muts$Gsub_LG2_PC1)>maxload1))
LG2end <- max(which(abs(muts$Gsub_LG2_PC1)>maxload1))

muts[LG2start ,]
##         chrom_full pos_full              Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 111433 NC_044049.1   481246 NC_044049.1__481246       NA       NA           NA
##        Gsub_LG2_PC1
## 111433   0.01027682
LG2start_minus1MB <-min(which(muts$chrom_full=="NC_044049.1"))
# in this case it's just the start of the chromosome
muts[LG2start_minus1MB,]
##         chrom_full pos_full           Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 109720 NC_044049.1      884 NC_044049.1__884       NA       NA           NA
##         Gsub_LG2_PC1
## 109720 -0.0006092057
muts[LG2end,]
##         chrom_full pos_full               Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 132871 NC_044049.1  4466546 NC_044049.1__4466546       NA       NA           NA
##        Gsub_LG2_PC1
## 132871   0.01029919
LG2end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG2end]+1000000 & muts$chrom_full=="NC_044049.1"))
muts[LG2end_plus1MB,]
##         chrom_full pos_full               Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 135332 NC_044049.1  5434591 NC_044049.1__5434591       NA       NA           NA
##        Gsub_LG2_PC1
## 135332 0.0002754641
plot(muts$pos_full[LG2start_minus1MB:LG2end_plus1MB], 
     abs(muts$Gsub_LG2_PC1[LG2start_minus1MB:LG2end_plus1MB]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG2", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG2start], col="orange", lwd=2)
abline(v=muts$pos_full[LG2end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")

Chrom 7

index <- sort(which(muts$chrom_full=="NC_044054.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012) 
set.seed(42348064)
svd7 <- big_randomSVD(Gsub_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)

muts$Gsub_LG7_PC1 <- NA
muts$Gsub_LG7_PC1[index] <- svd7$v[,1]

# Chrom 7
plot(muts$pos_full[muts$chrom_full=="NC_044054.1"], 
     abs(muts$Gsub_LG7_PC1[muts$chrom_full=="NC_044054.1"]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG7", ylab="PC1 loading", xlab="position (bp)")

(maxload1 <- quantile(abs(muts$Gsub_LG7_PC1), probs=0.99, na.rm=TRUE))
##         99% 
## 0.006244065
abline(h=maxload1)

#start
LG7start <- min(which(abs(muts$Gsub_LG7_PC1)>maxload1))
LG7end <- max(which(abs(muts$Gsub_LG7_PC1)>maxload1))

muts[LG7start ,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 648745 NC_044054.1 16828712 NC_044054.1__16828712       NA       NA
##        Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 648745           NA           NA -0.006261396
LG7start_minus1MB <-max(which(muts$pos_full<muts$pos_full[LG7start]-1000000 & muts$chrom_full=="NC_044054.1"))
# in this case it's just the start of the chromosome
muts[LG7start_minus1MB,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 645345 NC_044054.1 15828590 NC_044054.1__15828590       NA       NA
##        Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 645345           NA           NA 0.0002948823
muts[LG7end,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 696592 NC_044054.1 26336501 NC_044054.1__26336501       NA       NA
##        Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 696592           NA           NA -0.006245197
LG7end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG7end]+1000000 & muts$chrom_full=="NC_044054.1"))
muts[LG7end_plus1MB,]
##         chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 700639 NC_044054.1 27336483 NC_044054.1__27336483       NA       NA
##        Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1
## 700639           NA           NA -0.000523632
plot(muts$pos_full[LG7start_minus1MB:LG7end_plus1MB], 
     abs(muts$Gsub_LG7_PC1[LG7start_minus1MB:LG7end_plus1MB]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG7", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG7start], col="orange", lwd=2)
abline(v=muts$pos_full[LG7end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")

Chrom 12

index <- sort(which(muts$chrom_full=="NC_044059.1"))
Gsub <- G_full[,index]
# Recode for bigsnpr package tools
Gsub_snp <- add_code256(big_copy(Gsub,type="raw"),code=bigsnpr:::CODE_012) 
set.seed(73240982)
svd7 <- big_randomSVD(Gsub_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)

muts$Gsub_LG12_PC1 <- NA
muts$Gsub_LG12_PC1[index] <- svd7$v[,1]

# Chrom 12
plot(muts$pos_full[muts$chrom_full=="NC_044059.1"], 
     abs(muts$Gsub_LG12_PC1[muts$chrom_full=="NC_044059.1"]), 
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG12", ylab="PC1 loading", xlab="position (bp)")


(maxload1 <- quantile(abs(muts$Gsub_LG12_PC1), probs=0.99, na.rm=TRUE))
##         99% 
## 0.008958482
abline(h=maxload1)

#start
LG12start <- min(which(abs(muts$Gsub_LG12_PC1)>maxload1))
LG12end <- max(which(abs(muts$Gsub_LG12_PC1)>maxload1))

muts[LG12start ,]
##          chrom_full pos_full               Glabel Gsub_PC2 Gsub_PC1
## 1098771 NC_044059.1  1809214 NC_044059.1__1809214       NA       NA
##         Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1098771           NA           NA           NA  -0.008967974
LG12start_minus1MB <-max(which(muts$pos_full<muts$pos_full[LG12start]-1000000 & muts$chrom_full=="NC_044059.1"))
# in this case it's just the start of the chromosome
muts[LG12start_minus1MB,]
##          chrom_full pos_full              Glabel Gsub_PC2 Gsub_PC1 Gsub_LG1_PC1
## 1096496 NC_044059.1   721009 NC_044059.1__721009       NA       NA           NA
##         Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1096496           NA           NA  -0.004226609
muts[LG12end,]
##          chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 1141346 NC_044059.1 13690550 NC_044059.1__13690550       NA       NA
##         Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1141346           NA           NA           NA  -0.009079696
LG12end_plus1MB <- max(which(muts$pos_full<muts$pos_full[LG12end]+1000000 & muts$chrom_full=="NC_044059.1"))
muts[LG12end_plus1MB,]
##          chrom_full pos_full                Glabel Gsub_PC2 Gsub_PC1
## 1142816 NC_044059.1 14677663 NC_044059.1__14677663       NA       NA
##         Gsub_LG1_PC1 Gsub_LG2_PC1 Gsub_LG7_PC1 Gsub_LG12_PC1
## 1142816           NA           NA           NA  2.969367e-05
plot(muts$pos_full[LG12start_minus1MB:LG12end_plus1MB], 
     abs(muts$Gsub_LG12_PC1[LG12start_minus1MB:LG12end_plus1MB]),
     pch=19, col=adjustcolor("blue",0.1), 
     main="LG12", ylab="PC1 loading", xlab="position (bp)")
abline(v=muts$pos_full[LG12start], col="orange", lwd=2)
abline(v=muts$pos_full[LG12end], col="orange", lwd=2)
abline(h=maxload1, col="lightgrey")

summarize breakpoints

breakpoints <- data.frame(
  LG = c("LG1","LG2", "LG7","LG12"),
  LGstartIndex = c(LG1start,LG2start,LG7start,LG12start),
  LGendIndex = c(LG1end,LG2end,LG7end,LG12end),
  chrom=chrom_full[c(LG1start,LG2start,LG7start,LG12start)],
  LGstartPos = pos_full[c(LG1start,LG2start,LG7start,LG12start)],
  LGendPos = pos_full[c(LG1end,LG2end,LG7end,LG12end)],
  LGstartPos_minus1MB_index = c(LG1start_minus1MB,
                                LG2start_minus1MB,
                                LG7start_minus1MB,
                                LG12start_minus1MB),
  LGendPos_plus1MB_index =c(LG1end_plus1MB,
                                LG2end_plus1MB,
                                LG7end_plus1MB,
                                LG12end_plus1MB)
)

Add additional categories to sample df

samp_full$Ecotype2 <- factor(paste0(samp_full$Ecotype,"-",
                                 samp_full$Region), ordered=TRUE)
levels(samp_full$Ecotype2)
## [1] "1-Nearshore-GoM"     "1-Nearshore-Iceland" "2-Offshore-Iceland"
samp_full$Ecotype2_color <- samp_full$Ecotype2 
levels(samp_full$Ecotype2_color) <- c("lightblue","cornflowerblue","darkviolet")
levels(samp_full$Ecotype2_color)
## [1] "lightblue"      "cornflowerblue" "darkviolet"
str(samp_full$Ecotype2_color)
##  Ord.factor w/ 3 levels "lightblue"<"cornflowerblue"<..: 1 1 1 1 1 1 1 1 1 1 ...

PC just on inversions

Get all LG indexes

LGind <- c(LG1start:LG1end, LG2start:LG2end,
           LG7start:LG7end, LG12start:LG12end)

G_LG <- G_full[,LGind]

dim(G_full)
## [1]     294 2094293
G_nonInv <- G_full[,-LGind]
dim(G_nonInv)
## [1]     294 1911507
set.seed(34594323)
G_nonInv_subset <- G_nonInv[,sample(1:ncol(G_nonInv), 100000,
                                    replace=FALSE)]
dim(G_nonInv_subset)
## [1]    294 100000
saveRDS(G_nonInv_subset, file="../outputs/G_nonInv_subset.RDS")
write("This file contains a genotype matrix with 100000 SNPs randomly sampled from non-inversion regions, output from file KL-1 inversion code all.Rmd. The samples are in rows and the SNPs are in columns. Each cell stores the number of copies of the alternate allele.",
      "../outputs/G_nonInv_subset.metadata")

head(colnames(G_LG))
## [1] "NC_044048.1__11299038" "NC_044048.1__11299525" "NC_044048.1__11299592"
## [4] "NC_044048.1__11299650" "NC_044048.1__11302157" "NC_044048.1__11302179"
head(rownames(G_LG))
## [1] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216"
## [2] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220"
## [3] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224"
## [4] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225"
## [5] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229"
## [6] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231"
dim(G_LG)
## [1]    294 182786
# Recode for bigsnpr package tools
G_LG_snp <- add_code256(big_copy(G_LG,type="raw"),code=bigsnpr:::CODE_012) 

# PCA
# make sure this is run on a code 256 type
# snp object, or it will run forever!
set.seed(3459723)
svd7 <- big_randomSVD(G_LG_snp, 
                      snp_scaleBinom(), 
                      ncores = NCORES,
                      k=2)


samp_full$G_AllInv_PC1 <- svd7$u[,1]
samp_full$G_AllInv_PC2 <- svd7$u[,2]

str(samp_full)
## 'data.frame':    294 obs. of  15 variables:
##  $ samp_full     : int  16216 16220 16224 16225 16229 16231 16232 16233 16234 16236 ...
##  $ Pop           : Factor w/ 9 levels "Pop1","Pop2",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ PopID         : Ord.factor w/ 9 levels "GoM.Mass.Olive.Winter"<..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Region        : Factor w/ 2 levels "GoM","Iceland": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Ecotype       : Factor w/ 2 levels "1-Nearshore",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ label         : chr  "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225" ...
##  $ Region_color  : chr  "blue4" "blue4" "blue4" "blue4" ...
##  $ Ecotype_color : chr  "darkcyan" "darkcyan" "darkcyan" "darkcyan" ...
##  $ PopID_color   : chr  "#006400FF" "#006400FF" "#006400FF" "#006400FF" ...
##  $ Gsub_PC1      : num  -0.0589 -0.067 -0.0651 -0.0614 -0.0538 ...
##  $ Gsub_PC2      : num  0.02733 0.00134 0.00245 0.00487 0.0154 ...
##  $ Ecotype2      : Ord.factor w/ 3 levels "1-Nearshore-GoM"<..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Ecotype2_color: Ord.factor w/ 3 levels "lightblue"<"cornflowerblue"<..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ G_AllInv_PC1  : num  0.0353 0.065 0.0613 0.0515 0.0319 ...
##  $ G_AllInv_PC2  : num  -0.00791 -0.04903 -0.05377 -0.03753 0.01956 ...
pdf("../figures/PCA-samples-inversion-SNPs-only.pdf", width=6, height=6)
ggplot(samp_full) + geom_point(aes(x=G_AllInv_PC1,
                                   y=G_AllInv_PC2,
                                    colour = PopID,
                                   shape= Ecotype,
                                   pch=Ecotype,
                                   size=Ecotype)) +
    scale_colour_manual(values=pop.colors) +
      xlab("Sample loadings PC1 - inversion SNPs only") +
    ylab("Sample loadings PC2 - inversion SNPs only") +
  theme_classic()
## Warning: Duplicated aesthetics after name standardisation: shape
## Warning: Using size for a discrete variable is not advised.
## Warning: Duplicated aesthetics after name standardisation: shape
dev.off()
## quartz_off_screen 
##                 2
dist <- dist(G_LG, diag=TRUE)

str(dist)
##  'dist' num [1:43071] 297 281 298 287 256 ...
##  - attr(*, "Size")= int 294
##  - attr(*, "Labels")= chr [1:294] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225" ...
##  - attr(*, "Diag")= logi TRUE
##  - attr(*, "Upper")= logi FALSE
##  - attr(*, "method")= chr "euclidean"
##  - attr(*, "call")= language dist(x = G_LG, diag = TRUE)
hc <- hclust(dist)
str(hc)
## List of 7
##  $ merge      : int [1:293, 1:2] -21 -8 -54 -223 -193 -218 -151 -138 7 -166 ...
##  $ height     : num [1:293] 104 110 119 196 198 ...
##  $ order      : int [1:294] 146 258 230 147 172 238 243 142 164 156 ...
##  $ labels     : chr [1:294] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225" ...
##  $ method     : chr "complete"
##  $ call       : language hclust(d = dist)
##  $ dist.method: chr "euclidean"
##  - attr(*, "class")= chr "hclust"
dhc <- as.dendrogram(hc)
cut_avg <- cutree(hc, k = 5)
str(cut_avg)
##  Named int [1:294] 1 1 2 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:294] "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224" "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225" ...
str(dhc)
## --[dendrogram w/ 2 branches and 294 members at h = 554]
##   |--[dendrogram w/ 2 branches and 97 members at h = 375]
##   |  |--[dendrogram w/ 2 branches and 54 members at h = 275]
##   |  |  |--[dendrogram w/ 2 branches and 6 members at h = 219]
##   |  |  |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18014" 
##   |  |  |  `--[dendrogram w/ 2 branches and 5 members at h = 215]
##   |  |  |     |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18058" 
##   |  |  |     `--[dendrogram w/ 2 branches and 4 members at h = 211]
##   |  |  |        |--leaf "Iceland_2-Offshore_Ice.Off.NE_18122" 
##   |  |  |        `--[dendrogram w/ 2 branches and 3 members at h = 209]
##   |  |  |           |--leaf "Iceland_2-Offshore_Ice.Off.SW_18015" 
##   |  |  |           `--[dendrogram w/ 2 branches and 2 members at h = 206]
##   |  |  |              |--leaf "Iceland_2-Offshore_Ice.Off.SW_18047" 
##   |  |  |              `--leaf "Iceland_2-Offshore_Ice.Off.NE_18131" 
##   |  |  `--[dendrogram w/ 2 branches and 48 members at h = 234]
##   |  |     |--[dendrogram w/ 2 branches and 10 members at h = 214]
##   |  |     |  |--leaf "Iceland_2-Offshore_Ice.Off.NE_18138" 
##   |  |     |  `--[dendrogram w/ 2 branches and 9 members at h = 213]
##   |  |     |     |--[dendrogram w/ 2 branches and 4 members at h = 210]
##   |  |     |     |  |--[dendrogram w/ 2 branches and 2 members at h = 208]
##   |  |     |     |  |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18008" 
##   |  |     |     |  |  `--leaf "Iceland_2-Offshore_Ice.Off.SW_18038" 
##   |  |     |     |  `--[dendrogram w/ 2 branches and 2 members at h = 208]
##   |  |     |     |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18029" 
##   |  |     |     |     `--leaf "Iceland_2-Offshore_Ice.Off.NE_18118" 
##   |  |     |     `--[dendrogram w/ 2 branches and 5 members at h = 211]
##   |  |     |        |--leaf "Iceland_2-Offshore_Ice.Off.SW_18010" 
##   |  |     |        `--[dendrogram w/ 2 branches and 4 members at h = 209]
##   |  |     |           |--leaf "Iceland_2-Offshore_Ice.Off.SW_18044" 
##   |  |     |           `--[dendrogram w/ 2 branches and 3 members at h = 207]
##   |  |     |              |--leaf "Iceland_2-Offshore_Ice.Off.SW_18030" 
##   |  |     |              `--[dendrogram w/ 2 branches and 2 members at h = 204]
##   |  |     |                 |--leaf "Iceland_2-Offshore_Ice.Off.NE_18109" 
##   |  |     |                 `--leaf "Iceland_2-Offshore_Ice.Off.NE_18124" 
##   |  |     `--[dendrogram w/ 2 branches and 38 members at h = 219]
##   |  |        |--leaf "Iceland_2-Offshore_Ice.Off.NE_18140" 
##   |  |        `--[dendrogram w/ 2 branches and 37 members at h = 217]
##   |  |           |--leaf "Iceland_2-Offshore_Ice.Off.NE_18147" 
##   |  |           `--[dendrogram w/ 2 branches and 36 members at h = 213]
##   |  |              |--leaf "Iceland_2-Offshore_Ice.Off.NE_18146" 
##   |  |              `--[dendrogram w/ 2 branches and 35 members at h = 212]
##   |  |                 |--[dendrogram w/ 2 branches and 32 members at h = 211]
##   |  |                 |  |--[dendrogram w/ 2 branches and 30 members at h = 209]
##   |  |                 |  |  |--[dendrogram w/ 2 branches and 2 members at h = 207]
##   |  |                 |  |  |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18001" 
##   |  |                 |  |  |  `--leaf "Iceland_2-Offshore_Ice.Off.SW_18049" 
##   |  |                 |  |  `--[dendrogram w/ 2 branches and 28 members at h = 209]
##   |  |                 |  |     |--[dendrogram w/ 2 branches and 19 members at h = 207]
##   |  |                 |  |     |  |--[dendrogram w/ 2 branches and 12 members at h = 206]
##   |  |                 |  |     |  |  |--[dendrogram w/ 2 branches and 8 members at h = 203]
##   |  |                 |  |     |  |  |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18003" 
##   |  |                 |  |     |  |  |  `--[dendrogram w/ 2 branches and 7 members at h = 202]
##   |  |                 |  |     |  |  |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18141" 
##   |  |                 |  |     |  |  |     `--[dendrogram w/ 2 branches and 6 members at h = 201]
##   |  |                 |  |     |  |  |        |--[dendrogram w/ 2 branches and 4 members at h = 199]
##   |  |                 |  |     |  |  |        |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18021" 
##   |  |                 |  |     |  |  |        |  `--[dendrogram w/ 2 branches and 3 members at h = 198]
##   |  |                 |  |     |  |  |        |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18170" 
##   |  |                 |  |     |  |  |        |     `--[dendrogram w/ 2 branches and 2 members at h = 196]
##   |  |                 |  |     |  |  |        |        |--leaf "Iceland_2-Offshore_Ice.Off.NE_18113" 
##   |  |                 |  |     |  |  |        |        `--leaf "Iceland_2-Offshore_Ice.Off.NE_18128" 
##   |  |                 |  |     |  |  |        `--[dendrogram w/ 2 branches and 2 members at h = 200]
##   |  |                 |  |     |  |  |           |--leaf "Iceland_2-Offshore_Ice.Off.SW_18002" 
##   |  |                 |  |     |  |  |           `--leaf "Iceland_2-Offshore_Ice.Off.SW_18046" 
##   |  |                 |  |     |  |  `--[dendrogram w/ 2 branches and 4 members at h = 204]
##   |  |                 |  |     |  |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18013" 
##   |  |                 |  |     |  |     `--[dendrogram w/ 2 branches and 3 members at h = 203]
##   |  |                 |  |     |  |        |--leaf "Iceland_2-Offshore_Ice.Off.SW_18031" 
##   |  |                 |  |     |  |        `--[dendrogram w/ 2 branches and 2 members at h = 199]
##   |  |                 |  |     |  |           |--leaf "Iceland_2-Offshore_Ice.Off.NE_18106" 
##   |  |                 |  |     |  |           `--leaf "Iceland_2-Offshore_Ice.Off.NE_18133" 
##   |  |                 |  |     |  `--[dendrogram w/ 2 branches and 7 members at h = 206]
##   |  |                 |  |     |     |--[dendrogram w/ 2 branches and 5 members at h = 204]
##   |  |                 |  |     |     |  |--[dendrogram w/ 2 branches and 2 members at h = 202]
##   |  |                 |  |     |     |  |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18026" 
##   |  |                 |  |     |     |  |  `--leaf "Iceland_2-Offshore_Ice.Off.NE_18130" 
##   |  |                 |  |     |     |  `--[dendrogram w/ 2 branches and 3 members at h = 203]
##   |  |                 |  |     |     |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18025" 
##   |  |                 |  |     |     |     `--[dendrogram w/ 2 branches and 2 members at h = 201]
##   |  |                 |  |     |     |        |--leaf "Iceland_2-Offshore_Ice.Off.SW_18040" 
##   |  |                 |  |     |     |        `--leaf "Iceland_2-Offshore_Ice.Off.NE_18125" 
##   |  |                 |  |     |     `--[dendrogram w/ 2 branches and 2 members at h = 205]
##   |  |                 |  |     |        |--leaf "Iceland_2-Offshore_Ice.Off.SW_18034" 
##   |  |                 |  |     |        `--leaf "Iceland_2-Offshore_Ice.Off.NE_18149" 
##   |  |                 |  |     `--[dendrogram w/ 2 branches and 9 members at h = 208]
##   |  |                 |  |        |--[dendrogram w/ 2 branches and 3 members at h = 206]
##   |  |                 |  |        |  |--leaf "Iceland_2-Offshore_Ice.Off.NE_18103" 
##   |  |                 |  |        |  `--[dendrogram w/ 2 branches and 2 members at h = 203]
##   |  |                 |  |        |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18104" 
##   |  |                 |  |        |     `--leaf "Iceland_2-Offshore_Ice.Off.NE_18112" 
##   |  |                 |  |        `--[dendrogram w/ 2 branches and 6 members at h = 206]
##   |  |                 |  |           |--[dendrogram w/ 2 branches and 3 members at h = 205]
##   |  |                 |  |           |  |--leaf "Iceland_2-Offshore_Ice.Off.NE_18126" 
##   |  |                 |  |           |  `--[dendrogram w/ 2 branches and 2 members at h = 203]
##   |  |                 |  |           |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18108" 
##   |  |                 |  |           |     `--leaf "Iceland_2-Offshore_Ice.Off.NE_18151" 
##   |  |                 |  |           `--[dendrogram w/ 2 branches and 3 members at h = 206]
##   |  |                 |  |              |--leaf "Iceland_2-Offshore_Ice.Off.NE_18143" 
##   |  |                 |  |              `--[dendrogram w/ 2 branches and 2 members at h = 204]
##   |  |                 |  |                 |--leaf "Iceland_2-Offshore_Ice.Off.SW_18033" 
##   |  |                 |  |                 `--leaf "Iceland_2-Offshore_Ice.Off.SW_18039" 
##   |  |                 |  `--[dendrogram w/ 2 branches and 2 members at h = 210]
##   |  |                 |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18012" 
##   |  |                 |     `--leaf "Iceland_2-Offshore_Ice.Off.NE_18150" 
##   |  |                 `--[dendrogram w/ 2 branches and 3 members at h = 211]
##   |  |                    |--leaf "Iceland_2-Offshore_Ice.Off.SW_18051" 
##   |  |                    `--[dendrogram w/ 2 branches and 2 members at h = 208]
##   |  |                       |--leaf "Iceland_2-Offshore_Ice.Off.NE_18123" 
##   |  |                       `--leaf "Iceland_2-Offshore_Ice.Off.NE_18139" 
##   |  `--[dendrogram w/ 2 branches and 43 members at h = 344]
##   |     |--[dendrogram w/ 2 branches and 28 members at h = 299]
##   |     |  |--[dendrogram w/ 2 branches and 4 members at h = 249]
##   |     |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18152" 
##   |     |  |  `--[dendrogram w/ 2 branches and 3 members at h = 243]
##   |     |  |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18119" 
##   |     |  |     `--[dendrogram w/ 2 branches and 2 members at h = 229]
##   |     |  |        |--leaf "Iceland_2-Offshore_Ice.Off.NE_18117" 
##   |     |  |        `--leaf "Iceland_2-Offshore_Ice.Off.NE_18148" 
##   |     |  `--[dendrogram w/ 2 branches and 24 members at h = 269]
##   |     |     |--[dendrogram w/ 2 branches and 21 members at h = 236]
##   |     |     |  |--leaf "Iceland_2-Offshore_Ice.Off.NE_18127" 
##   |     |     |  `--[dendrogram w/ 2 branches and 20 members at h = 232]
##   |     |     |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18142" 
##   |     |     |     `--[dendrogram w/ 2 branches and 19 members at h = 229]
##   |     |     |        |--[dendrogram w/ 2 branches and 17 members at h = 226]
##   |     |     |        |  |--[dendrogram w/ 2 branches and 3 members at h = 225]
##   |     |     |        |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18075" 
##   |     |     |        |  |  `--[dendrogram w/ 2 branches and 2 members at h = 223]
##   |     |     |        |  |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18017" 
##   |     |     |        |  |     `--leaf "Iceland_2-Offshore_Ice.Off.SW_18032" 
##   |     |     |        |  `--[dendrogram w/ 2 branches and 14 members at h = 225]
##   |     |     |        |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18037" 
##   |     |     |        |     `--[dendrogram w/ 2 branches and 13 members at h = 224]
##   |     |     |        |        |--leaf "Iceland_2-Offshore_Ice.Off.SW_18019" 
##   |     |     |        |        `--[dendrogram w/ 2 branches and 12 members at h = 221]
##   |     |     |        |           |--[dendrogram w/ 2 branches and 7 members at h = 220]
##   |     |     |        |           |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18048" 
##   |     |     |        |           |  `--[dendrogram w/ 2 branches and 6 members at h = 219]
##   |     |     |        |           |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18024" 
##   |     |     |        |           |     `--[dendrogram w/ 2 branches and 5 members at h = 217]
##   |     |     |        |           |        |--leaf "Iceland_2-Offshore_Ice.Off.NE_18132" 
##   |     |     |        |           |        `--[dendrogram w/ 2 branches and 4 members at h = 216]
##   |     |     |        |           |           |--leaf "Iceland_2-Offshore_Ice.Off.SW_18006" 
##   |     |     |        |           |           `--[dendrogram w/ 2 branches and 3 members at h = 214]
##   |     |     |        |           |              |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18093" 
##   |     |     |        |           |              `--[dendrogram w/ 2 branches and 2 members at h = 211]
##   |     |     |        |           |                 |--leaf "Iceland_2-Offshore_Ice.Off.SW_18041" 
##   |     |     |        |           |                 `--leaf "Iceland_2-Offshore_Ice.Off.NE_18115" 
##   |     |     |        |           `--[dendrogram w/ 2 branches and 5 members at h = 221]
##   |     |     |        |              |--[dendrogram w/ 2 branches and 3 members at h = 217]
##   |     |     |        |              |  |--leaf "Iceland_2-Offshore_Ice.Off.SW_18022" 
##   |     |     |        |              |  `--[dendrogram w/ 2 branches and 2 members at h = 215]
##   |     |     |        |              |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18005" 
##   |     |     |        |              |     `--leaf "Iceland_2-Offshore_Ice.Off.SW_18043" 
##   |     |     |        |              `--[dendrogram w/ 2 branches and 2 members at h = 218]
##   |     |     |        |                 |--leaf "Iceland_2-Offshore_Ice.Off.SW_18020" 
##   |     |     |        |                 `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18081" 
##   |     |     |        `--[dendrogram w/ 2 branches and 2 members at h = 227]
##   |     |     |           |--leaf "Iceland_2-Offshore_Ice.Off.NE_18116" 
##   |     |     |           `--leaf "Iceland_2-Offshore_Ice.Off.NE_18120" 
##   |     |     `--[dendrogram w/ 2 branches and 3 members at h = 242]
##   |     |        |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18186" 
##   |     |        `--[dendrogram w/ 2 branches and 2 members at h = 228]
##   |     |           |--leaf "Iceland_2-Offshore_Ice.Off.NE_18136" 
##   |     |           `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18083" 
##   |     `--[dendrogram w/ 2 branches and 15 members at h = 313]
##   |        |--[dendrogram w/ 2 branches and 3 members at h = 246]
##   |        |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18187" 
##   |        |  `--[dendrogram w/ 2 branches and 2 members at h = 226]
##   |        |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18160" 
##   |        |     `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18078" 
##   |        `--[dendrogram w/ 2 branches and 12 members at h = 247]
##   |           |--[dendrogram w/ 2 branches and 3 members at h = 223]
##   |           |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18052" 
##   |           |  `--[dendrogram w/ 2 branches and 2 members at h = 218]
##   |           |     |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18059" 
##   |           |     `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18091" 
##   |           `--[dendrogram w/ 2 branches and 9 members at h = 233]
##   |              |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18099" 
##   |              `--[dendrogram w/ 2 branches and 8 members at h = 232]
##   |                 |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18082" 
##   |                 `--[dendrogram w/ 2 branches and 7 members at h = 230]
##   |                    |--[dendrogram w/ 2 branches and 5 members at h = 225]
##   |                    |  |--leaf "Iceland_2-Offshore_Ice.Off.NE_18110" 
##   |                    |  `--[dendrogram w/ 2 branches and 4 members at h = 223]
##   |                    |     |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18100" 
##   |                    |     `--[dendrogram w/ 2 branches and 3 members at h = 220]
##   |                    |        |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18096" 
##   |                    |        `--[dendrogram w/ 2 branches and 2 members at h = 219]
##   |                    |           |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18193" 
##   |                    |           `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18088" 
##   |                    `--[dendrogram w/ 2 branches and 2 members at h = 227]
##   |                       |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18159" 
##   |                       `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18162" 
##   `--[dendrogram w/ 2 branches and 197 members at h = 466]
##      |--[dendrogram w/ 2 branches and 21 members at h = 363]
##      |  |--[dendrogram w/ 2 branches and 4 members at h = 307]
##      |  |  |--[dendrogram w/ 2 branches and 2 members at h = 237]
##      |  |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17016" 
##      |  |  |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17283" 
##      |  |  `--[dendrogram w/ 2 branches and 2 members at h = 252]
##      |  |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17285" 
##      |  |     `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17008" 
##      |  `--[dendrogram w/ 2 branches and 17 members at h = 332]
##      |     |--[dendrogram w/ 2 branches and 3 members at h = 262]
##      |     |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18056" 
##      |     |  `--[dendrogram w/ 2 branches and 2 members at h = 240]
##      |     |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18155" 
##      |     |     `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18061" 
##      |     `--[dendrogram w/ 2 branches and 14 members at h = 306]
##      |        |--[dendrogram w/ 2 branches and 5 members at h = 257]
##      |        |  |--[dendrogram w/ 2 branches and 2 members at h = 229]
##      |        |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18070" 
##      |        |  |  `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18094" 
##      |        |  `--[dendrogram w/ 2 branches and 3 members at h = 234]
##      |        |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18180" 
##      |        |     `--[dendrogram w/ 2 branches and 2 members at h = 229]
##      |        |        |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18188" 
##      |        |        `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18086" 
##      |        `--[dendrogram w/ 2 branches and 9 members at h = 278]
##      |           |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16241" 
##      |           `--[dendrogram w/ 2 branches and 8 members at h = 252]
##      |              |--[dendrogram w/ 2 branches and 5 members at h = 232]
##      |              |  |--[dendrogram w/ 2 branches and 3 members at h = 229]
##      |              |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18084" 
##      |              |  |  `--[dendrogram w/ 2 branches and 2 members at h = 228]
##      |              |  |     |--leaf "Iceland_2-Offshore_Ice.Off.SW_18042" 
##      |              |  |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18185" 
##      |              |  `--[dendrogram w/ 2 branches and 2 members at h = 231]
##      |              |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18154" 
##      |              |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18175" 
##      |              `--[dendrogram w/ 2 branches and 3 members at h = 233]
##      |                 |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18179" 
##      |                 `--[dendrogram w/ 2 branches and 2 members at h = 230]
##      |                    |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18161" 
##      |                    `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18090" 
##      `--[dendrogram w/ 2 branches and 176 members at h = 401]
##         |--[dendrogram w/ 2 branches and 99 members at h = 368]
##         |  |--[dendrogram w/ 2 branches and 10 members at h = 299]
##         |  |  |--[dendrogram w/ 2 branches and 4 members at h = 250]
##         |  |  |  |--[dendrogram w/ 2 branches and 2 members at h = 228]
##         |  |  |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18189" 
##         |  |  |  |  `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18077" 
##         |  |  |  `--[dendrogram w/ 2 branches and 2 members at h = 230]
##         |  |  |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18171" 
##         |  |  |     `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18065" 
##         |  |  `--[dendrogram w/ 2 branches and 6 members at h = 270]
##         |  |     |--[dendrogram w/ 2 branches and 3 members at h = 234]
##         |  |     |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18062" 
##         |  |     |  `--[dendrogram w/ 2 branches and 2 members at h = 225]
##         |  |     |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18173" 
##         |  |     |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18190" 
##         |  |     `--[dendrogram w/ 2 branches and 3 members at h = 241]
##         |  |        |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18164" 
##         |  |        `--[dendrogram w/ 2 branches and 2 members at h = 219]
##         |  |           |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18194" 
##         |  |           `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18092" 
##         |  `--[dendrogram w/ 2 branches and 89 members at h = 358]
##         |     |--[dendrogram w/ 2 branches and 40 members at h = 302]
##         |     |  |--[dendrogram w/ 2 branches and 22 members at h = 254]
##         |     |  |  |--[dendrogram w/ 2 branches and 8 members at h = 249]
##         |     |  |  |  |--[dendrogram w/ 2 branches and 2 members at h = 246]
##         |     |  |  |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17311" 
##         |     |  |  |  |  `--leaf "GoM_1-Nearshore_GoM.Mass.Red_16211" 
##         |     |  |  |  `--[dendrogram w/ 2 branches and 6 members at h = 247]
##         |     |  |  |     |--[dendrogram w/ 2 branches and 3 members at h = 244]
##         |     |  |  |     |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16227" 
##         |     |  |  |     |  `--[dendrogram w/ 2 branches and 2 members at h = 241]
##         |     |  |  |     |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16248" 
##         |     |  |  |     |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17240" 
##         |     |  |  |     `--[dendrogram w/ 2 branches and 3 members at h = 244]
##         |     |  |  |        |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17273" 
##         |     |  |  |        `--[dendrogram w/ 2 branches and 2 members at h = 239]
##         |     |  |  |           |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17324" 
##         |     |  |  |           `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17288" 
##         |     |  |  `--[dendrogram w/ 2 branches and 14 members at h = 251]
##         |     |  |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220" 
##         |     |  |     `--[dendrogram w/ 2 branches and 13 members at h = 249]
##         |     |  |        |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17028" 
##         |     |  |        `--[dendrogram w/ 2 branches and 12 members at h = 247]
##         |     |  |           |--[dendrogram w/ 2 branches and 3 members at h = 242]
##         |     |  |           |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16238" 
##         |     |  |           |  `--[dendrogram w/ 2 branches and 2 members at h = 237]
##         |     |  |           |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16240" 
##         |     |  |           |     `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17292" 
##         |     |  |           `--[dendrogram w/ 2 branches and 9 members at h = 244]
##         |     |  |              |--[dendrogram w/ 2 branches and 4 members at h = 239]
##         |     |  |              |  |--[dendrogram w/ 2 branches and 2 members at h = 236]
##         |     |  |              |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17010" 
##         |     |  |              |  |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17265" 
##         |     |  |              |  `--[dendrogram w/ 2 branches and 2 members at h = 236]
##         |     |  |              |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17210" 
##         |     |  |              |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17226" 
##         |     |  |              `--[dendrogram w/ 2 branches and 5 members at h = 242]
##         |     |  |                 |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17248" 
##         |     |  |                 `--[dendrogram w/ 2 branches and 4 members at h = 239]
##         |     |  |                    |--[dendrogram w/ 2 branches and 2 members at h = 235]
##         |     |  |                    |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17253" 
##         |     |  |                    |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17258" 
##         |     |  |                    `--[dendrogram w/ 2 branches and 2 members at h = 237]
##         |     |  |                       |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17002" 
##         |     |  |                       `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17245" 
##         |     |  `--[dendrogram w/ 2 branches and 18 members at h = 259]
##         |     |     |--[dendrogram w/ 2 branches and 7 members at h = 243]
##         |     |     |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17206" 
##         |     |     |  `--[dendrogram w/ 2 branches and 6 members at h = 239]
##         |     |     |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17033" 
##         |     |     |     `--[dendrogram w/ 2 branches and 5 members at h = 236]
##         |     |     |        |--[dendrogram w/ 2 branches and 2 members at h = 232]
##         |     |     |        |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17304" 
##         |     |     |        |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17270" 
##         |     |     |        `--[dendrogram w/ 2 branches and 3 members at h = 236]
##         |     |     |           |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231" 
##         |     |     |           `--[dendrogram w/ 2 branches and 2 members at h = 231]
##         |     |     |              |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16234" 
##         |     |     |              `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17276" 
##         |     |     `--[dendrogram w/ 2 branches and 11 members at h = 248]
##         |     |        |--[dendrogram w/ 2 branches and 2 members at h = 207]
##         |     |        |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17308" 
##         |     |        |  `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17309" 
##         |     |        `--[dendrogram w/ 2 branches and 9 members at h = 245]
##         |     |           |--[dendrogram w/ 2 branches and 6 members at h = 239]
##         |     |           |  |--[dendrogram w/ 2 branches and 2 members at h = 235]
##         |     |           |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216" 
##         |     |           |  |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17280" 
##         |     |           |  `--[dendrogram w/ 2 branches and 4 members at h = 238]
##         |     |           |     |--[dendrogram w/ 2 branches and 2 members at h = 235]
##         |     |           |     |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_16219" 
##         |     |           |     |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17211" 
##         |     |           |     `--[dendrogram w/ 2 branches and 2 members at h = 236]
##         |     |           |        |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17007" 
##         |     |           |        `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17256" 
##         |     |           `--[dendrogram w/ 2 branches and 3 members at h = 242]
##         |     |              |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17242" 
##         |     |              `--[dendrogram w/ 2 branches and 2 members at h = 234]
##         |     |                 |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16242" 
##         |     |                 `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17306" 
##         |     `--[dendrogram w/ 2 branches and 49 members at h = 339]
##         |        |--[dendrogram w/ 2 branches and 10 members at h = 294]
##         |        |  |--[dendrogram w/ 2 branches and 5 members at h = 242]
##         |        |  |  |--[dendrogram w/ 2 branches and 3 members at h = 237]
##         |        |  |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18064" 
##         |        |  |  |  `--[dendrogram w/ 2 branches and 2 members at h = 232]
##         |        |  |  |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18182" 
##         |        |  |  |     `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18097" 
##         |        |  |  `--[dendrogram w/ 2 branches and 2 members at h = 241]
##         |        |  |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18183" 
##         |        |  |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18184" 
##         |        |  `--[dendrogram w/ 2 branches and 5 members at h = 253]
##         |        |     |--[dendrogram w/ 2 branches and 3 members at h = 231]
##         |        |     |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18165" 
##         |        |     |  `--[dendrogram w/ 2 branches and 2 members at h = 228]
##         |        |     |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18166" 
##         |        |     |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18174" 
##         |        |     `--[dendrogram w/ 2 branches and 2 members at h = 239]
##         |        |        |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18172" 
##         |        |        `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18191" 
##         |        `--[dendrogram w/ 2 branches and 39 members at h = 316]
##         |           |--[dendrogram w/ 2 branches and 7 members at h = 272]
##         |           |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229" 
##         |           |  `--[dendrogram w/ 2 branches and 6 members at h = 260]
##         |           |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17286" 
##         |           |     `--[dendrogram w/ 2 branches and 5 members at h = 248]
##         |           |        |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17224" 
##         |           |        `--[dendrogram w/ 2 branches and 4 members at h = 244]
##         |           |           |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17260" 
##         |           |           `--[dendrogram w/ 2 branches and 3 members at h = 238]
##         |           |              |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17155" 
##         |           |              `--[dendrogram w/ 2 branches and 2 members at h = 235]
##         |           |                 |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17314" 
##         |           |                 `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17281" 
##         |           `--[dendrogram w/ 2 branches and 32 members at h = 281]
##         |              |--[dendrogram w/ 2 branches and 22 members at h = 257]
##         |              |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16232" 
##         |              |  `--[dendrogram w/ 2 branches and 21 members at h = 252]
##         |              |     |--[dendrogram w/ 2 branches and 19 members at h = 250]
##         |              |     |  |--[dendrogram w/ 2 branches and 5 members at h = 247]
##         |              |     |  |  |--[dendrogram w/ 2 branches and 2 members at h = 110]
##         |              |     |  |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16233" 
##         |              |     |  |  |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17233" 
##         |              |     |  |  `--[dendrogram w/ 2 branches and 3 members at h = 245]
##         |              |     |  |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17262" 
##         |              |     |  |     `--[dendrogram w/ 2 branches and 2 members at h = 239]
##         |              |     |  |        |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17221" 
##         |              |     |  |        `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17252" 
##         |              |     |  `--[dendrogram w/ 2 branches and 14 members at h = 249]
##         |              |     |     |--[dendrogram w/ 2 branches and 4 members at h = 246]
##         |              |     |     |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17031" 
##         |              |     |     |  `--[dendrogram w/ 2 branches and 3 members at h = 245]
##         |              |     |     |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17254" 
##         |              |     |     |     `--[dendrogram w/ 2 branches and 2 members at h = 243]
##         |              |     |     |        |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17024" 
##         |              |     |     |        `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16228" 
##         |              |     |     `--[dendrogram w/ 2 branches and 10 members at h = 247]
##         |              |     |        |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16236" 
##         |              |     |        `--[dendrogram w/ 2 branches and 9 members at h = 245]
##         |              |     |           |--[dendrogram w/ 2 branches and 3 members at h = 242]
##         |              |     |           |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17268" 
##         |              |     |           |  `--[dendrogram w/ 2 branches and 2 members at h = 239]
##         |              |     |           |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17327" 
##         |              |     |           |     `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17316" 
##         |              |     |           `--[dendrogram w/ 2 branches and 6 members at h = 244]
##         |              |     |              |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225" 
##         |              |     |              `--[dendrogram w/ 2 branches and 5 members at h = 240]
##         |              |     |                 |--[dendrogram w/ 2 branches and 3 members at h = 236]
##         |              |     |                 |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17027" 
##         |              |     |                 |  `--[dendrogram w/ 2 branches and 2 members at h = 234]
##         |              |     |                 |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17294" 
##         |              |     |                 |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17272" 
##         |              |     |                 `--[dendrogram w/ 2 branches and 2 members at h = 237]
##         |              |     |                    |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17313" 
##         |              |     |                    `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17279" 
##         |              |     `--[dendrogram w/ 2 branches and 2 members at h = 251]
##         |              |        |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17026" 
##         |              |        `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17153" 
##         |              `--[dendrogram w/ 2 branches and 10 members at h = 263]
##         |                 |--[dendrogram w/ 2 branches and 3 members at h = 247]
##         |                 |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16247" 
##         |                 |  `--[dendrogram w/ 2 branches and 2 members at h = 238]
##         |                 |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17230" 
##         |                 |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17259" 
##         |                 `--[dendrogram w/ 2 branches and 7 members at h = 248]
##         |                    |--[dendrogram w/ 2 branches and 3 members at h = 244]
##         |                    |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17271" 
##         |                    |  `--[dendrogram w/ 2 branches and 2 members at h = 241]
##         |                    |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17032" 
##         |                    |     `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17019" 
##         |                    `--[dendrogram w/ 2 branches and 4 members at h = 247]
##         |                       |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17257" 
##         |                       `--[dendrogram w/ 2 branches and 3 members at h = 243]
##         |                          |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17204" 
##         |                          `--[dendrogram w/ 2 branches and 2 members at h = 236]
##         |                             |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16239" 
##         |                             `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17282" 
##         `--[dendrogram w/ 2 branches and 77 members at h = 384]
##            |--[dendrogram w/ 2 branches and 30 members at h = 320]
##            |  |--[dendrogram w/ 2 branches and 12 members at h = 268]
##            |  |  |--[dendrogram w/ 2 branches and 5 members at h = 249]
##            |  |  |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17238" 
##            |  |  |  `--[dendrogram w/ 2 branches and 4 members at h = 245]
##            |  |  |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17287" 
##            |  |  |     `--[dendrogram w/ 2 branches and 3 members at h = 241]
##            |  |  |        |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17234" 
##            |  |  |        `--[dendrogram w/ 2 branches and 2 members at h = 236]
##            |  |  |           |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17236" 
##            |  |  |           `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17249" 
##            |  |  `--[dendrogram w/ 2 branches and 7 members at h = 262]
##            |  |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17261" 
##            |  |     `--[dendrogram w/ 2 branches and 6 members at h = 252]
##            |  |        |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17011" 
##            |  |        `--[dendrogram w/ 2 branches and 5 members at h = 242]
##            |  |           |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17219" 
##            |  |           `--[dendrogram w/ 2 branches and 4 members at h = 237]
##            |  |              |--[dendrogram w/ 2 branches and 2 members at h = 232]
##            |  |              |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16245" 
##            |  |              |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17215" 
##            |  |              `--[dendrogram w/ 2 branches and 2 members at h = 235]
##            |  |                 |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17326" 
##            |  |                 `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17325" 
##            |  `--[dendrogram w/ 2 branches and 18 members at h = 277]
##            |     |--[dendrogram w/ 2 branches and 11 members at h = 257]
##            |     |  |--[dendrogram w/ 2 branches and 3 members at h = 232]
##            |     |  |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18098" 
##            |     |  |  `--[dendrogram w/ 2 branches and 2 members at h = 223]
##            |     |  |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18153" 
##            |     |  |     `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18156" 
##            |     |  `--[dendrogram w/ 2 branches and 8 members at h = 243]
##            |     |     |--leaf "Iceland_2-Offshore_Ice.Off.NE_18134" 
##            |     |     `--[dendrogram w/ 2 branches and 7 members at h = 238]
##            |     |        |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18158" 
##            |     |        `--[dendrogram w/ 2 branches and 6 members at h = 236]
##            |     |           |--[dendrogram w/ 2 branches and 2 members at h = 233]
##            |     |           |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18080" 
##            |     |           |  `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18095" 
##            |     |           `--[dendrogram w/ 2 branches and 4 members at h = 233]
##            |     |              |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18067" 
##            |     |              `--[dendrogram w/ 2 branches and 3 members at h = 231]
##            |     |                 |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18072" 
##            |     |                 `--[dendrogram w/ 2 branches and 2 members at h = 230]
##            |     |                    |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18053" 
##            |     |                    `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18101" 
##            |     `--[dendrogram w/ 2 branches and 7 members at h = 261]
##            |        |--[dendrogram w/ 2 branches and 2 members at h = 237]
##            |        |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18163" 
##            |        |  `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18167" 
##            |        `--[dendrogram w/ 2 branches and 5 members at h = 242]
##            |           |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18085" 
##            |           `--[dendrogram w/ 2 branches and 4 members at h = 234]
##            |              |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18178" 
##            |              `--[dendrogram w/ 2 branches and 3 members at h = 234]
##            |                 |--leaf "Iceland_2-Offshore_Ice.Off.SW_18035" 
##            |                 `--[dendrogram w/ 2 branches and 2 members at h = 231]
##            |                    |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18069" 
##            |                    `--leaf "Iceland_1-Nearshore_Ice.Near.NE_18087" 
##            `--[dendrogram w/ 2 branches and 47 members at h = 356]
##               |--[dendrogram w/ 2 branches and 3 members at h = 287]
##               |  |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18076" 
##               |  `--[dendrogram w/ 2 branches and 2 members at h = 251]
##               |     |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17203" 
##               |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17218" 
##               `--[dendrogram w/ 2 branches and 44 members at h = 333]
##                  |--[dendrogram w/ 2 branches and 6 members at h = 262]
##                  |  |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18168" 
##                  |  `--[dendrogram w/ 2 branches and 5 members at h = 244]
##                  |     |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18176" 
##                  |     `--[dendrogram w/ 2 branches and 4 members at h = 233]
##                  |        |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18073" 
##                  |        `--[dendrogram w/ 2 branches and 3 members at h = 229]
##                  |           |--leaf "Iceland_1-Nearshore_Ice.Near.NE_18074" 
##                  |           `--[dendrogram w/ 2 branches and 2 members at h = 224]
##                  |              |--leaf "Iceland_1-Nearshore_Ice.Near.SW_18157" 
##                  |              `--leaf "Iceland_1-Nearshore_Ice.Near.SW_18192" 
##                  `--[dendrogram w/ 2 branches and 38 members at h = 312]
##                     |--[dendrogram w/ 2 branches and 10 members at h = 259]
##                     |  |--[dendrogram w/ 2 branches and 2 members at h = 240]
##                     |  |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_16218" 
##                     |  |  `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17278" 
##                     |  `--[dendrogram w/ 2 branches and 8 members at h = 248]
##                     |     |--[dendrogram w/ 2 branches and 3 members at h = 243]
##                     |     |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17264" 
##                     |     |  `--[dendrogram w/ 2 branches and 2 members at h = 233]
##                     |     |     |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17017" 
##                     |     |     `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17156" 
##                     |     `--[dendrogram w/ 2 branches and 5 members at h = 245]
##                     |        |--[dendrogram w/ 2 branches and 2 members at h = 240]
##                     |        |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17006" 
##                     |        |  `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17029" 
##                     |        `--[dendrogram w/ 2 branches and 3 members at h = 243]
##                     |           |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17296" 
##                     |           `--[dendrogram w/ 2 branches and 2 members at h = 104]
##                     |              |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17291" 
##                     |              `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16221" 
##                     `--[dendrogram w/ 2 branches and 28 members at h = 269]
##                        |--[dendrogram w/ 2 branches and 5 members at h = 243]
##                        |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17003" 
##                        |  `--[dendrogram w/ 2 branches and 4 members at h = 242]
##                        |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17298" 
##                        |     `--[dendrogram w/ 2 branches and 3 members at h = 239]
##                        |        |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16249" 
##                        |        `--[dendrogram w/ 2 branches and 2 members at h = 236]
##                        |           |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17001" 
##                        |           `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17277" 
##                        `--[dendrogram w/ 2 branches and 23 members at h = 257]
##                           |--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17216" 
##                           `--[dendrogram w/ 2 branches and 22 members at h = 254]
##                              |--[dendrogram w/ 2 branches and 2 members at h = 119]
##                              |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17022" 
##                              |  `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17023" 
##                              `--[dendrogram w/ 2 branches and 20 members at h = 251]
##                                 |--[dendrogram w/ 2 branches and 8 members at h = 244]
##                                 |  |--[dendrogram w/ 2 branches and 3 members at h = 241]
##                                 |  |  |--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17267" 
##                                 |  |  `--[dendrogram w/ 2 branches and 2 members at h = 240]
##                                 |  |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17289" 
##                                 |  |     `--leaf "GoM_1-Nearshore_GoM.Cashes.Red_17263" 
##                                 |  `--[dendrogram w/ 2 branches and 5 members at h = 244]
##                                 |     |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17303" 
##                                 |     `--[dendrogram w/ 2 branches and 4 members at h = 241]
##                                 |        |--[dendrogram w/ 2 branches and 2 members at h = 234]
##                                 |        |  |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17020" 
##                                 |        |  `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17290" 
##                                 |        `--[dendrogram w/ 2 branches and 2 members at h = 235]
##                                 |           |--leaf "GoM_1-Nearshore_GoM.Mass.Red_16214" 
##                                 |           `--leaf "GoM_1-Nearshore_GoM.Mass.Red_17013" 
##                                 `--[dendrogram w/ 2 branches and 12 members at h = 249]
##                                    |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17018" 
##                                    `--[dendrogram w/ 2 branches and 11 members at h = 246]
##                                       |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_17030" 
##                                       `--[dendrogram w/ 2 branches and 10 members at h = 243]
##                                          |--[dendrogram w/ 2 branches and 4 members at h = 239]
##                                          |  |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16243" 
##                                          |  `--[dendrogram w/ 2 branches and 3 members at h = 237]
##                                          |     |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17154" 
##                                          |     `--[dendrogram w/ 2 branches and 2 members at h = 232]
##                                          |        |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Unknown_16223" 
##                                          |        `--leaf "GoM_1-Nearshore_GoM.Cashes.Olive_17235" 
##                                          `--[dendrogram w/ 2 branches and 6 members at h = 243]
##                                             |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224" 
##                                             `--[dendrogram w/ 2 branches and 5 members at h = 240]
##                                                |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17015" 
##                                                `--[dendrogram w/ 2 branches and 4 members at h = 238]
##                                                   |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17315" 
##                                                   `--[dendrogram w/ 2 branches and 3 members at h = 236]
##                                                      |--leaf "GoM_1-Nearshore_GoM.Mass.Red_17005" 
##                                                      `--[dendrogram w/ 2 branches and 2 members at h = 233]
##                                                         |--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17305" 
##                                                         `--leaf "GoM_1-Nearshore_GoM.Mass.Olive.Winter_17317"
# https://www.datacamp.com/tutorial/hierarchical-clustering-R
pdf("../figures/Hclust-inversionSNPsonly.pdf", width=15, height=10)
plot(hc, cex=0.3)
rect.hclust(hc , k = 5, border=2:6)
dev.off()
## quartz_off_screen 
##                 2
samp_full$InvHclustOrder <- hc$order
samp_full$InvHclustK5 <- as.numeric(cut_avg)

# this looks like SW near in Iceland is more closely related to GOM then NE NEar in Iceland
table(samp_full$PopID, samp_full$InvHclustK5)
##                         
##                           1  2  3  4  5
##   GoM.Mass.Olive.Winter  22  9  2  1  0
##   GoM.Mass.Red           15 17  2  1  0
##   GoM.Mass.Olive.Unknown  9  5  0  3  0
##   GoM.Cashes.Olive       14  5  0  6  0
##   GoM.Cashes.Red         19  4  1  1  0
##   Ice.Off.SW              0  0  1  1 37
##   Ice.Near.SW            14  4  8  6  8
##   Ice.Off.NE              0  0  0  1 38
##   Ice.Near.NE             6  3  7 10 14
pdf("../figures/Hclust-inversionSNPsonly-heatmap.pdf", width=15, height=15)
par(oma=c(8,4,4,8))
heatmap(as.matrix(dist), cexRow=0.2, cexCol=0.2, scale="none", ColSideColors=samp_full$PopID_color, RowSideColors=samp_full$PopID_color, )
dev.off()
## quartz_off_screen 
##                 2

save outputs

head(samp_full)
##   samp_full  Pop                 PopID Region     Ecotype
## 1     16216 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 2     16220 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 3     16224 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 4     16225 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 5     16229 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
## 6     16231 Pop1 GoM.Mass.Olive.Winter    GoM 1-Nearshore
##                                         label Region_color Ecotype_color
## 1 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216        blue4      darkcyan
## 2 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220        blue4      darkcyan
## 3 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224        blue4      darkcyan
## 4 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225        blue4      darkcyan
## 5 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229        blue4      darkcyan
## 6 GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231        blue4      darkcyan
##   PopID_color    Gsub_PC1    Gsub_PC2        Ecotype2 Ecotype2_color
## 1   #006400FF -0.05893059 0.027334412 1-Nearshore-GoM      lightblue
## 2   #006400FF -0.06696424 0.001338206 1-Nearshore-GoM      lightblue
## 3   #006400FF -0.06511353 0.002449571 1-Nearshore-GoM      lightblue
## 4   #006400FF -0.06136966 0.004868653 1-Nearshore-GoM      lightblue
## 5   #006400FF -0.05381484 0.015398091 1-Nearshore-GoM      lightblue
## 6   #006400FF -0.05952850 0.018067312 1-Nearshore-GoM      lightblue
##   G_AllInv_PC1 G_AllInv_PC2 InvHclustOrder InvHclustK5
## 1   0.03531921 -0.007908553            146           1
## 2   0.06496404 -0.049032057            258           1
## 3   0.06134477 -0.053768027            230           2
## 4   0.05153129 -0.037532901            147           1
## 5   0.03185495  0.019557487            172           1
## 6   0.04147050  0.003228003            238           1
write.csv(samp_full,"../outputs/1-Samples.csv")
saveRDS(samp_full,"../outputs/1-Samples.rds")
write("This file describes information about each sample. It is saved as an RDS file for loading into R with the proper column objects (e.g. ordered factors) ",
      "../outputs/1-Samples.metadata")

Save individual inversion files

breakpoints
##     LG LGstartIndex LGendIndex       chrom LGstartPos LGendPos
## 1  LG1        33090     104012 NC_044048.1   11299038 28292263
## 2  LG2       111433     132871 NC_044049.1     481246  4466546
## 3  LG7       648745     696592 NC_044054.1   16828712 26336501
## 4 LG12      1098771    1141346 NC_044059.1    1809214 13690550
##   LGstartPos_minus1MB_index LGendPos_plus1MB_index
## 1                     29750                 106154
## 2                    109720                 135332
## 3                    645345                 700639
## 4                   1096496                1142816
write.csv(breakpoints, "../outputs/1-breakpoints.csv", row.names = FALSE)
write("This file describes the breakpoint of inversions identified by the 99% outlier PCA loadings for individual chromsome /n
      LG: linkage group /n
      LGstartIndex: Start index of the inversion in the full genotype matrix stored in `1-AllGSNPs.rds` /n
      LGendIndex: end index of the inversion in the full genotype matrix stored in `1-AllGSNPs.rds` /n
      chrom: chromosome /n
      LGstartPos: start position of the inversion on the chromosoms /n
      LGendPos: end start position of the inversion on the chromosoms /n
      LGstartPos_minus1MB_index: Start index minus 1 MB of the inversion in the full genotype matrix stored in `1-AllGSNPs.rds` /n
      LGendPos_plus1MB_index: end index plus 1MB of the inversion in the full genotype matrix stored in `1-AllGSNPs.rds` /n",
      "../outputs/1-breakpoints.csv.metadata.md")

head(G_full[,1:5]) # make sure rows and columns are labeled
##                                             NC_044048.1__268 NC_044048.1__280
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216                0                2
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220                1                2
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224                1                2
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225                0                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229                1                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231                1                1
##                                             NC_044048.1__378 NC_044048.1__539
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216                0                1
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220                0                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224                0                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225                0                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229                0                0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231                0                0
##                                             NC_044048.1__1555
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16216                 0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16220                 0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16224                 0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16225                 0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16229                 0
## GoM_1-Nearshore_GoM.Mass.Olive.Winter_16231                 0
saveRDS(G_LG, "../outputs/1-AllLGSNPs.rds")
dim(G_LG)
## [1]    294 182786
write("This file is a genotype matrix for SNPs located in the four inversions
      Each matrix has individuals in rows and SNPs in columns
      Each cell has the number of copies of the alternate allele",
      "../outputs/1-AllLGSNPs.metadata.md")


saveRDS(G_full[,LG1start_minus1MB:LG1end_plus1MB], "../outputs/1-G_LG1.rds")
saveRDS(G_full[,LG2start_minus1MB:LG2end_plus1MB], "../outputs/1-G_LG2.rds")
saveRDS(G_full[,LG7start_minus1MB:LG7end_plus1MB], "../outputs/1-G_LG7.rds")
saveRDS(G_full[,LG12start_minus1MB:LG12end_plus1MB], "../outputs/1-G_LG12.rds")
write("These files are genotype matrices for the inversions on each linkage group
      Each matrix has individuals in rows and SNPs in columns
      Each cell has the number of copies of the alternate allele",
      "../outputs/1-G_LGX.metadata.md")